subset.phylo: blending information from taxonomies and trees

In mwpennell/geiger-v2: Analysis of Evolutionary Diversification

blending information from taxonomies and trees

Description

working with systematic reference tables and phylogenies

Usage

    ## S3 method for class 'phylo'
subset(x, taxonomy, rank="", ncores=1, ...)

Arguments

x	a phylogenetic tree of class 'phylo'
taxonomy	a ('matrix') linkage table between tips of the phylogeny and clades represented in the tree; rownames of 'taxonomy' should be tips found in the phylogeny
rank	a column name in 'taxonomy' at which to resample the tree (see Examples)
ncores	max number of cores to use
...	arguments to be passed to other functions (has no effect in the present context)

Author(s)

JM Eastman

Examples

## Not run: 
sal <- get(data(caudata))
print(head(sal$tax))

nphy <- subset(sal$phy, sal$tax, "genus", ncores=1)
plot(nphy, type="fan", cex=0.15)

## End(Not run)

mwpennell/geiger-v2 documentation built on Feb. 26, 2023, 1:19 a.m.